Damn, good analysis, totally forgot that an open hatch due to breakers would prevent boost. Good pickup!
YES, I believe this is what happened to me that explains a lot! What I don't get was 'I was never scanned' prior to the limpet attack as I said the NPC literally appeared from nowhere I had no warnings at all except when the malfunctions started happening and cargo started disappearing.
On a different note, if limpets just go thur shields like they are not even there why the heck doesn't someone in this far future smarten up and just arm them with mini nuke warheads? Beats missiles!